From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Sun Apr 01 2012 - 12:03:17 CDT
Partly solved. I.e., I had forgot to renumber the atoms in
relationship to the other ligands.
There is now Fe-O bond. However, that oxygen is also protonated, in
spite of starting from pdb TYR without HH and stating "DELETE ATOM HH"
in the patch.
Thanks for suggesting how to avoid that HH.
francesco pietra
On Sun, Apr 1, 2012 at 4:53 PM, Francesco Pietra <chiendarret_at_gmail.com> wrote:
> Hi:
> By using psfgen, I am trying to get iron(II) of heme bound to also the
> para-O atom (OH) of tyrosine.
>
> Starting from pdb with fully protonated tyrosine, what I get is Fe-H-O- bonding.
>
> Removing the HH atom of tyrosine from pdb, no bond.
>
> On stating "DELETE ATOM HH" in the patch, again no bond, while the HH
> atom is added to the OH atom, irrespective of the protonation state of
> tyrosine.
>
> Thanks for pointing out what obvious I am overlooking.
>
> The tentative patch is (don't pay attention to the partial charges)
>
> GROUP !
> ATOM 1CB CT2 -0.18 ! 1HD1 1HE1 uncoord -0.18
> ATOM 1HB1 HA 0.09 ! | | 0.09
> ATOM 1HB2 HA 0.09 ! 1HB1 1CD1--1CE1 0.09
> GROUP ! | // \\
> ATOM 1CG CA 0.00 ! -1CB--1CG 1CZ--1OH 0.00
> GROUP ! | \ __ / \
> ATOM 1CD1 CA -0.115 ! 1HB2 1CD2--1CE2 2FE- -0.115
> ATOM 1HD1 HP 0.115 ! | | 0.115
> GROUP ! 1HD2 1HE2
> ATOM 1CE1 CA -0.115 ! -0.115
> ATOM 1HE1 HP 0.115 ! 0.115
> GROUP !
> ATOM 1CZ CA 0.115 ! 0.115
> ATOM 1OH OH1 -0.54 ! -0.51
> GROUP !
> ATOM 1CD2 CA -0.115 ! -0.115
> ATOM 1HD2 HP 0.115 ! 0.115
> GROUP !
> ATOM 1CE2 CA -0.115 ! -0.115
> ATOM HE2 HP 0.115 ! 0.115
> DELETE ANGLE 2NA 2FE 2NC 2NB 2FE 2ND
> DELETE ATOM HH
> BOND 1OH 2FE
> ANGLE 1CZ 1OH 2FE 1OH 2FE %NA 1OH 2FE 2NB 1OH 2FE 2NC
> ANGLE 1OH 2FE 2ND
> IC 1CZ 1OH 2FE 2NA 0.0000 0.0000 0.0000 0.0000 0.0000
> IC 1CZ 1OH 2FE 2NB 0.0000 0.0000 0.0000 0.0000 0.0000
> IC 1CZ 1OH 2FE 2NB 0.0000 0.0000 0.0000 0.0000 0.0000
> IC 1CZ 1OH 2FE 2NB 0.0000 0.0000 0.0000 0.0000 0.0000
> IC 1CZ 1OH 2FE 2NA 0.0000 0.0000 0.0000 0.0000 0.0000
>
> francesco pietra
>
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